Gist is, if we have a couple of fossils in a group of species we're interested in, but we want to know more about when species in this group diverged, we can use amounts of genetic divergence, coupled with molecular clock estimates, to fill in those dates.

Regarding neutral vs. non-neutral genetic loci: neutral (or nearly neutral) loci are good at letting us determine relationships. This is precisely because they are neutral; they change at more or less the same rate regardless of the rate of morphological or non-neutral site evolution, and so they give us unbiased estimates. Using genetic loci that are adaptively important lets us answer completely different questions. The main interest in studying non-neutral sites is in linking them to particular evolutionary changes. Those loci aren't good for inferring relationships, and, because they evolve at varying rates they can't be used in molecular clocks.

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